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qim3d

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    QIM3D (Quantitative Imaging in 3D)

    qim3D is a Python library for quantitative imaging analysis in 3D. It provides functionality for handling data, as well as tools for visualization and analysis.

    This library contains the tools and functionalities of the QIM platform, accessible at https://qim.dk/platform

    Installation

    Install the latest stable version by using pip:

    pip install qim3d

    Or clone this repository for the most recent version.

    Usage

    Some basic funtionalites are descibred here. The full documentation is still under development.

    Loading Data

    To load image data from a file, use qim.io.load()

    import qim3d
    
    # Load a file
    vol = qim3d.io.load("path/to/file.tif")
    
    # Load a file as a virtual stack
    vol = qim3d.io.load("path/to/file.tif", virtual_stack=True)

    Visualize data

    You can easily check slices from your volume using slices

    import qim3d
    
    img = qim3d.examples.fly_150x256x256
    
    # By default shows the middle slice
    qim3d.viz.slices(img)
    
    # Or we can specifly positions
    qim3d.viz.slices(img, position=[0,32,128])
    
    # Parameters for size and colormap are also possible
    qim3d.viz.slices(img, img_width=6, img_height=6, cmap="inferno")
    

    GUI Components

    The library also provides GUI components for interactive data analysis and exploration. The qim3d.gui module contains various classes for visualization and analysis:

    import qim3d
    
    app = qim3d.gui.iso3d.Interface()
    app.launch()

    GUIs can also be launched using the Qim3D CLI:

    $ qim3d gui --data-explorer

    Contributing

    Contributions to qim3d are welcome! If you find a bug, have a feature request, or would like to contribute code, please open an issue or submit a pull request.

    License

    This project is licensed under the MIT License.